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Background

Quasispecies (WIKIPEDIA-Viral quasispecies: http://en.wikipedia.org/wiki/Viral_quasispecies)

• populations of a virus within its host
• related to RNA viruses, which have very high mutation rates
• selection acts only on mutations, instead of individual sequences
• can't predict the evolution based on the fittest sequences

Antigenic Drift ((1)WIKIPEDIA-Antigenic drift: http://en.wikipedia.org/wiki/Antigenic_drift; (2) BMC Bioinformatics 2001, 2:1)

• first introduced for Inflenza HA
• accumulated mutations on the surface of HA
• it can escape host immune responses attack

Identify Selection and Measure Host Immune Responses

• a big challenge
  
• difficult to exploit evolutionary histories of virus
• accumulated mutations on cerntain regions may mask the detection of selection
• can't determine actual replacement mutations